Saenredam was born in Zaandam. As an orphan Jan lived with his uncle, Pieter de Jongh, a bailiff in Assendelft who first sent him to learn basket weaving as a profession.[1] Being an apt student, he was taught reading and writing, but astonished his teachers when he proved already so accomplished in this that he decorated his texts with curled decorations. An example of his penmanship could once be seen on display at Assum House near Heemskerk (residence of the Lord of Assendelft), which was his copywork of the ten commandments.[1] Despite a decision that he follow a career in a trade or farming, he showed such artistic talent that he started as an apprentice cartographer. His first map is dated 1589 and is of the province of Holland, which could be seen in the city book of Guiccardijn (referring to a 1593 work by Lodovico Guicciardini called The Description of the Low Countries).[1] He was visited by a lawyer called Spoorwater tot Assendelft, who convinced his guardian to let him apply his gift, and thus young Saenredam was sent to learn drawing from Hendrick Goltzius in Haarlem, where he became a master at the age of 24 (in 1589).[1]

According to the Rijksmuseum, he returned in 1595 from Amsterdam to Assendelft, where he married Anna Pauwelsdochter.[3] Jan left his wife a sizeable estate as a result of lucrative investments in the Dutch East India Company.[4] He died of typhus on April 6, 1607 and was buried in the choir of the Saint Adolphus church at Assendelft, with the gravestone inscription Ioannis Saenredam Sculptoris celeberrimi.[2] He died in Assendelft, aged about 41.